It could be due to a misunderstanding. For example, if some false information was spread about Konoha planning to harm Naruto or Kushina. They might act out of self - defense and overreact to the point of trying to destroy the village.
One possible motive could be that they were somehow brainwashed. Maybe an enemy with powerful genjutsu got to them and made them believe that Konoha was a threat that needed to be eliminated.
One possible motive could be a deep misunderstanding. Maybe Naruto is framed for something he didn't do, and the Konoha ninjas turn against him. In his desperation to prove his innocence and defend himself, he might end up accidentally killing some of them.
Perhaps a mind - control situation. Maybe an enemy was able to manipulate Naruto's mind, making him think that Konoha was an evil place that needed to be eradicated. It could be a powerful genjutsu or some other form of mind - influencing technique.
In fanfiction, Naruto might kill Konoha if he's under some sort of mind control. Maybe an enemy manages to manipulate his thoughts and turn him against the village. Also, if Naruto experiences a great loss because of Konoha's actions or inactions. Say, if his friends are killed due to Konoha's negligence in protecting them, and he blames the village as a whole. Or if he realizes that Konoha's system is so corrupt that it's causing more harm than good to the world.
One possible motive could be a misunderstanding. Maybe Haku was disguised as someone else who was about to attack Naruto or his friends, and Naruto reacted in self - defense without realizing it was Haku. Another could be that in this fanfiction, Naruto has been somehow corrupted or influenced by a dark force that made him lose his normal judgment and attack Haku.
It could be that his siblings have made a pact with an extremely evil entity. Naruto, with his sense of justice and loyalty to the greater good, decides that their existence in that state is too dangerous and kills them, though it would be a very difficult and heart - wrenching decision for him.
Another reason could be related to a prophecy. There might be a prophecy that Boruto will bring great destruction in the future, and Naruto, as the Hokage, feels it's his duty to prevent this at all costs. He might think that by killing Boruto, he can change the course of fate and protect the people he loves and the entire ninja world.
One possible reason could be for Naruto's safety. Maybe she has to go on a dangerous mission and believes Konoha is the safest place for him. Another reason might be that she is forced by some powerful enemies who threaten Naruto's life if she doesn't leave him in Konoha.
One possible motive could be mind control. Maybe an enemy used some powerful genjutsu on Naruto, making him lose his true self and turn against the Uzumaki clan. It's a common trope in fanfictions where the hero is forced to do something unthinkable.
One possible motive could be a major misunderstanding. Maybe Naruto was under some kind of mind - control or false information that made him believe the Uchiha clan was a threat to the village on a much greater scale than they actually were. So, in an attempt to protect the village, he took extreme action.
One possible motive could be that the angel attendant was working for an enemy force that Naruto perceived as a threat to his village. So, in order to protect his home and the people he loves, he might take such a drastic step.